## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[ctl1-R1.subsampled.80.merged.filt.bam] OUTPUT=ctl1-R1.subsampled.80.merged.dupmark.bam METRICS_FILE=ctl1-R1.subsampled.80.merged.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT USE_JDK_DEFLATER=true USE_JDK_INFLATER=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Nov 15 23:27:22 UTC 2019

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	0	14825	0	0	0	30	0	0.002024	3658067

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14765	14765
2.0	1.995956	30	30
3.0	2.987883	0	0
4.0	3.975798	0	0
5.0	4.959718	0	0
6.0	5.939659	0	0
7.0	6.915636	0	0
8.0	7.887666	0	0
9.0	8.855764	0	0
10.0	9.819947	0	0
11.0	10.780231	0	0
12.0	11.73663	0	0
13.0	12.689161	0	0
14.0	13.63784	0	0
15.0	14.582682	0	0
16.0	15.523703	0	0
17.0	16.460917	0	0
18.0	17.394342	0	0
19.0	18.32399	0	0
20.0	19.249879	0	0
21.0	20.172023	0	0
22.0	21.090438	0	0
23.0	22.005138	0	0
24.0	22.916138	0	0
25.0	23.823454	0	0
26.0	24.727101	0	0
27.0	25.627092	0	0
28.0	26.523444	0	0
29.0	27.41617	0	0
30.0	28.305286	0	0
31.0	29.190806	0	0
32.0	30.072744	0	0
33.0	30.951115	0	0
34.0	31.825934	0	0
35.0	32.697214	0	0
36.0	33.564971	0	0
37.0	34.429218	0	0
38.0	35.289969	0	0
39.0	36.147239	0	0
40.0	37.001043	0	0
41.0	37.851392	0	0
42.0	38.698303	0	0
43.0	39.541788	0	0
44.0	40.381862	0	0
45.0	41.218538	0	0
46.0	42.05183	0	0
47.0	42.881752	0	0
48.0	43.708318	0	0
49.0	44.53154	0	0
50.0	45.351433	0	0
51.0	46.16801	0	0
52.0	46.981284	0	0
53.0	47.791269	0	0
54.0	48.597977	0	0
55.0	49.401424	0	0
56.0	50.20162	0	0
57.0	50.998581	0	0
58.0	51.792317	0	0
59.0	52.582844	0	0
60.0	53.370174	0	0
61.0	54.154319	0	0
62.0	54.935292	0	0
63.0	55.713107	0	0
64.0	56.487776	0	0
65.0	57.259312	0	0
66.0	58.027728	0	0
67.0	58.793036	0	0
68.0	59.555248	0	0
69.0	60.314378	0	0
70.0	61.070437	0	0
71.0	61.823439	0	0
72.0	62.573395	0	0
73.0	63.320317	0	0
74.0	64.064219	0	0
75.0	64.805112	0	0
76.0	65.543009	0	0
77.0	66.277921	0	0
78.0	67.009861	0	0
79.0	67.738841	0	0
80.0	68.464872	0	0
81.0	69.187967	0	0
82.0	69.908137	0	0
83.0	70.625395	0	0
84.0	71.339751	0	0
85.0	72.051219	0	0
86.0	72.759808	0	0
87.0	73.465532	0	0
88.0	74.168402	0	0
89.0	74.868429	0	0
90.0	75.565625	0	0
91.0	76.260001	0	0
92.0	76.951568	0	0
93.0	77.640339	0	0
94.0	78.326323	0	0
95.0	79.009534	0	0
96.0	79.689981	0	0
97.0	80.367676	0	0
98.0	81.04263	0	0
99.0	81.714854	0	0
100.0	82.384359	0	0